A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with
set_mo_source(). They will all be searched when using
as.mo() and consequently all the
A data.frame with 5,605 observations and 2 variables:
Commonly used code of a microorganism
ID of the microorganism in the microorganisms data set
All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this
AMR package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find all download links on our website, which is automatically updated with every code change.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, http://www.catalogueoflife.org). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, lpsn.dsmz.de). This supplementation is needed until the CoL+ project is finished, which we await.
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.